October 10, 2009

Two bottlenecks shaped human genetic diversity

Proceedings of the Royal Society B doi:10.1098/rspb.2009.1473

Evidence that two main bottleneck events shaped modern human genetic diversity

W. Amos and J. I. Hoffman

Abstract

There is a strong consensus that modern humans originated in Africa and moved out to colonize the world approximately 50 000 years ago. During the process of expansion, variability was lost, creating a linear gradient of decreasing diversity with increasing distance from Africa. However, the exact way in which this loss occurred remains somewhat unclear: did it involve one, a few or a continuous series of population bottlenecks? We addressed this by analysing a large published dataset of 783 microsatellite loci genotyped in 53 worldwide populations, using the program ‘Bottleneck’. Immediately following a sharp population decline, rare alleles are lost faster than heterozygosity, creating a transient excess of heterozygosity relative to allele number, a feature that is used by Bottleneck to infer historical events.We find evidence of two primary events, one ‘out of Africa’ and one placed around the Bering Strait, where an ancient land bridge allowed passage into the Americas. These findings agree well with the regions of the world where the largest founder events might have been expected, but contrast with the apparently smooth gradient of variability that is revealed when current heterozygosity is plotted against distance from Africa.

8 comments:

Thanks for the link, Dienekes, this looks interesting. However, it's hard to see the Out of Africa bottleneck as the source of human biological/ cultural diversity.

If Out-of-Africa were the source of human diversity then the diversity we see today in Asia, Europe and Oceania would be completely unstructured, with little to no correlation between either genetic, morphological or cultural typology and geography. It comes too soon. And the Bering Strait bottleneck comes too late.

As I see it, there must have been a major bottleneck that developed somewhere on the Indian Ocean coast during the original OOA migration, roughly in the area of India and Pakistan. Such a bottleneck would explain a great many things, including the musical evidence that most interests me, but also the existence of certain genetic, morphological and cultural gaps between Africa and SE Asia and Melanesia.

Such a bottleneck could have been caused by the Toba explosion, but only if modern humans had already left colonies throughout the Indian Ocean coast, all the way to Sahul. A major Tsunami just south of India could have had a similar effect. I can think of no other explanation for the highly structured human diversity we find today.

By the way, you and your readers might find some of the most recent posts on my blog of interest, since I have been challenging some of the most sacrosanct assumptions of Anthropology there, and developing a completely new model of cultural evolution. I'd very much appreciate feedback from knowledgeable anthropologists and archaeologists: http://music000001.blogspot.com/Thanks, Victor

Very sensible comment, Victor. Luis also made a good observation on anthropology.net (http://anthropology.net/2009/10/08/evidence-that-two-main-bottleneck-events-shaped-modern-human-genetic-diversity-proc-r-soc-b-firstcite/#comments) regarding this paper. Amerindians are the least bottlenecked populations, according to Fig. 4.

Can anyone tell the location of the microsatelites? Y chromosome? Mitochondrial? Autosomal? The link seems to be broken.

Also where does 50K come from? I thought 50,000 years was the figure for the oldest male ancestor for the Out of Africa populations. Not the date of the Out of Africa migration which was older ~80,000 years.

Yes, Annie, 50,000 years doesn't sound right at all. Yet it's a figure that comes up often in the literature. Steven Oppenheimer's estimate is closer to 80,000 years, which to me makes a lot of sense, especially since it places modern humans on the Asiatic coast during the Toba eruption, ca. 72,000 ya. But Stanley Ambrose strongly disputes Oppenheimer's estimate -- and his interpretation of the Toba event. I corresponded briefly with him about this, but never got a satisfactory answer. According to Ambrose, all the evidence points away from such an early departure from Africa -- but when asked what that evidence was, he failed to respond. And in all that time since I've never been able to figure out what that "evidence" could be.

If no modern humans were in Asia when Toba exploded, then it's hard to see how the Toba event could have triggered the sort of human diversity Ambrose sees as its effect. I think he wants to see Toba as the trigger of human evolutionary "advancement," leading to the expansion into Asia. As I see it, the expansion into Asia is much more likely to have been simply a contingent event with no special immediate significance. In any case, if humans left Africa for Asia as late as 50,000 years ago, it's hard to see how they could have been present in Australia around the same time or in Europe only a few thousand years later.

With Europe, it is unlikely any modern European is descended from the AMH that entered it at the putative date of 40 to 50 kya. Many assumptions are made from using the dna of modern human populations and extrapolating backwards in time. For Europe, the 40 to 50 kya is somewhat shaky. Most Europeans descend from humans who entered Europe starting from around 20 kya with a large group entering just after the LGM and the Neolithic. The date that the ancestors of Australian Aborigines entered Australia is disputed and is considered more around 40 kya, but with other later colonisations.

Africans, that is sub Saharan Africans to be precise did experience bottlenecks. In the Autosomal marker DXYS156, the X allele spread is most diverse in sub Saharan Africans but the Y allele is most diverse in East Asians.

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